Kill Switch
by MacGateFan
Summary: AU of Lifeline and there after. Shep/Weir. Elizabeth survives the initial attack on the Replicator planet only for McKay and Sheppard to use the Kill Switch once she's been beamed to the Apollo, however she survives...


Title: Kill Switch

Rating: PG

Author: MacGateFan

Disclaimers: Unfortunately they're not mine.

* * *

Elizabeth was still holding Oberoth and the Replicators in stasis by the time John and Ronon had reached the Jumper. She could feel them invading her mind, attempting to take control of it.

No! She silently cried. Elizabeth was not going down without a fight! Before she knew it she felt the familiar sensation of being transported. She looked around and saw that she was in the Apollo's brig.

John and Rodney were staring at her and she realized that the beaming caused the Replicators to take control of her body.

"John, the Kill Switch."

"What? Elizabeth, no, we don't need to!"

Elizabeth felt the tears in her eyes threatening to spill over. She knew exactly how John felt because she felt the same way. However she knew she couldn't remain alive no matter how much she wanted to.

"John, they're taking over as we speak. If you don't... then I won't be able to control them."

Rodney looked at them both with wild eyes. His hands were tightly holding onto the tablet containing the Kill Switch. "We can't...! Elizabeth, I can help you! Let me!"

"Please," she whispered, squeezing her eyes shut. "John."

"Give me the tablet, Rodney."

Rodney stared at him in shock, eyes red. "What? Are you nuts? John, I can help her!"

"It's too late, Rodney," John said, pain evident in his voice. "We have to do this or they'll have complete control over her and we're screwed."

Reluctantly, Rodney handed him the tablet. He was about to drop to the floor when Ronon came up beside him and patted him on the back. Rodney nodded, knowing this was for the best but hating it completely.

John's heart thundered in chest as moved towards the brig. "Open it."

Elizabeth looked up when she heard the door open, tears were falling freely now. "Thank you, John," she whispered, kissing him softly on the lips. "I love you."

John nodded, typing in his authorization code. "I love you too, Elizabeth," he said.

Once the Kill Switch was activated, she was falling to her knees and John helped her to the floor."I guess it wasn't such a great idea for us to admit this now," Elizabeth told him, reaching up to touch his face. "I'm sorry, John."

"Yeah, we probably should have said it a long time ago. I'm sorry too, Elizabeth."

Instead of replying Elizabeth smiled up at him and closed her eyes. John lifted her close and held her tight. The pain he was feeling right now was overwhelming. He never knew something could hurt so much. He felt a hand on his shoulder but he didn't want to let go of her... not yet.

"Sheppard."

"I got her, thanks," John replied, lifting her from the floor.

There was silence as John carried Elizabeth through the corridors of the Apollo and to the infirmary. As he laid her on one of the beds, he felt her breathing. He turned to Rodney and Ronon, who had followed him.

"Please tell me I'm not imagining this."

"What?" Rodney asked.

"She's... she's breathing."

Rodney glanced back at Ronon, worried his friend was starting to flip out. "That's impossible," he said, taking her wrist to check her pulse. "Once the kill switch was activated it would... Oh my God! She has a pulse! She's alive!"

Ronon ran to the office where the ship's doctor was. "Hey, we need some help out here!" he said.

"What's going on?" the doctor asked, rushing out and over to Elizabeth.

"Rodney," John said, nudging him towards the doctor.

"Right. She was injected with nanites to heal her earlier injuries. We created a kill switch that would essentially deactivate them and cause her... her death. Thing is, she's still alive so she's gonna need treatment. Oh, and guards."

John looked at him. "Guards?"

"Yes, guards," Rodney said. "Sheppard, we don't know if those things are dead. If not, then there's a chance that the Replicators are on their way. She may even try to sabotage the ship if we just leave her alone."

He nodded slowly. "But she wouldn't be alone. I won't be leaving her side anytime soon."

* * *

John waited impatiently for Dr. Keller to complete her exam of Elizabeth. Dr. Braxton from the Apollo said that there were signs of a coma but without the proper equipment there wasn't anyway to tell how serious it was. He was so lost in thought that he nearly ran into Rodney.

"I don't even know how you were able to get us onto this planet," he said. "That must've taken a lot out of you."

John merely shrugged and Rodney was finally able to get a good look at his friend. It was just as he suspected. John's face was pale and drawn. The chair and the landing really did him in but John Sheppard wasn't going to rest until he knew Elizabeth was going to be all right.

"Look, you're not going to help her if you collapse yourself, John. Get some sleep. I'll call you if anything important happens."

John was thoughtful for the moment but finally gave in. "All right, I will. But the minute you hear..."

"I got it."

"Thanks, Rodney," John replied before leaving the infirmary.

A few minutes after John left, Keller came out. "Where' s Colonel Sheppard?" she asked.

"I convinced him to get some sleep. How's Elizabeth?"

Jennifer sighed. This was the part about being a doctor she hated. "Elizabeth has slipped into a coma, Rodney. It's bad. Really bad. I don't believe she'll ever wake up and if there's a remote chance that she does, she's going to have a significant amount of brain damage."

"So basically we're back where we started."

"It looks that way. Although the nanites have stopped working so there's no threat there."

Rodney closed his eyes, taking a deep breath. "I guess that's something, huh?"

* * *

Sam found John sitting on a chair, head resting on Elizabeth's bed. She hated being the bearer of bad news but it had been almost a month and she was still in a deep coma. The IOA felt it necessary to have her brought back to Earth.

"John," she said, placing a hand on his shoulder. He stirred and lifted his head, blinking away the sleep in his eyes. "Sorry to bother you."

John stretched but once he looked at Sam, he knew something was wrong. "What happened?"

"They're sending her back to Earth, John."

"What?" he asked, his voice barely above a whisper. "They can't do that!"

Sam sighed. John had to have known this was inevitable. "We don't have the resources to care for her here," she told him. "You know that."

John looked back at Elizabeth, taking her hand in his. "I know. I guess I was just hoping this day would never come."

"I understand."

"When does she leave?"

Sam took a deep breath. "Tomorrow morning."

John was thoughtful for a minute before speaking up. "Um... I don't supposed I could go too. Make sure she's comfortable and..."

"Permission granted, John. Take as much time as you need."

"Thanks."

* * *

It had only been a few days when John was called back to Atlantis. Daniel promised to visit Elizabeth when he wasn't off world and John appreciated it. All the members of SG-1 were greatly understanding.

The IOA wanted John to become the head of Atlantis as Colonel Carter was needed on Earth. He wasn't sure about their decision but he guessed it was better if he were charge instead of someone from the IOA themselves.

John hovered near Elizabeth's bed minutes before he the Apollo was to pick him up. "I don't know how often I'll be able to visit you," John said, his voice thick with emotion. "Just remember, no matter what, that I love you. I will always love you, Elizabeth."

He leaned in to kiss her softly on the lips. "Always."

"John?"

John straightened, still holding tight to Elizabeth's hand. "Daniel," he replied.

"The Apollo just arrived in orbit. They'll be ready as soon as they re-supply." He nodded and turned back to face Elizabeth. "She'll be fine, John."

"Yeah, I know. She'll get the best medical care possible." He paused and Daniel thought he was going to say more. "Take care of her for me, please?"

"I promise."

John took a deep breath and walked out of the room. "Apollo this is Sheppard. Ready to beam aboard."

* * *

"I can't believe they put Sheppard in charge!"

"Rodney," Teyla admonished.

"Oh no! It's not that I don't think he can do the job, I just mean that he won't be going off world with us anymore."

Teyla frowned. She hadn't thought about that. "What does this mean?" she asked.

"We're going to get someone else to be our team's leader. Probably Major Lorne since he's next in command." Rodney shrugged. "I guess he'll be fine. Better than most anyway."

"Why Doc I didn't even know you cared."

Rodney turned to see Lorne standing there with a grin on his face. He turned back to face Teyla and Ronon. "A little warning next time!"

"The Apollo's arrived in orbit," Sam said. A few minutes later, John was beamed into the Gateroom. "Welcome back to Atlantis, John."

"Thanks," he replied. The smile he wore never reached his eyes. Although John had to admit, it was good to be back. He only wished Elizabeth could be there with him.

Teyla moved forward to grab his arms and they leaned their foreheads in to touch. "How is Elizabeth?" she asked.

"Still the same."

"She is strong, John," Teyla told him. "After all, she has you."

John nodded, but he wasn't so certain. What the hell could he do a galaxy away?

* * *

John sat back in Elizabeth's chair with a sigh. It would never be his chair. Even though he's sat in it for the past two months and even though he would probably been in it in the foreseeable future, it would always be Elizabeth's chair.

He glanced at the computer when it beeped. His team... Correction... Major Lorne's team was due to return in five minutes as long as trouble didn't find them. John stood and stretched and was relieved to hear the alarms go off signaling an off world activation.

"Chuck?"

"It's Major Lorne's IDC, Sir."

At John's nod, Chuck lowered the shield. He watched with mild amusement how the team came back, scowls on their faces and covered in mud. He was half tempted to tell them debriefing was now, but he really didn't want them tracking all that mud up the stairs.

"We'll debrief at 0900 tomorrow morning, Major," John said, stifling a laugh.

Lorne glanced back at Rodney, who cowered behind Teyla, then back up at John. "Yes, Sir!"

Once they were gone, the 'Gate activated again. "It's the SGC, Colonel."

John's heart skipped a beat. He hoped that didn't mean... No, Elizabeth was fine!

"Patch it through, Chuck."

"Sir, they're asking us to lower the shield. They're sending someone through."

"Who?"

Chuck shrugged. "They won't say."

John ran to the top of the stairs when that 'someone' came through the 'Gate, he had to try to restrain himself. Instead he took a deep breath and slowly walked down to her. There was nothing he could do about the grin plastered on his face.

Elizabeth was returning John's smile. All eyes were on the them and if the expedition didn't know their feelings before, they certainly knew now. "When did you... how did...?"

"A speechless John Sheppard," Elizabeth replied. "That's something I never thought I'd see."

John looked around the Gateroom and nodded to everyone. They immediately began to clap. "Welcome home, Elizabeth."

"Thank you, John."

So, what did you think? Should I continue this?? Do you want more?? Please let me know. I have some ideas.  
Mac


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